NUTM1-Rearranged Infant and Pediatric B Cell Precursor Acute Lymphoblastic Leukemia: A Good Prognostic Subtype Identified in a Collaborative International Study

Background and Aims A novel genetic subtype of B cell precursor acute lymphoblastic leukemia (B-ALL) is characterized by rearrangement of NUTM1 (NUTM1r) on 15q14 resulting in fusion of NUTM1 to one of several partner genes such as CUX1, ACIN1, BRD9, and IKZF1. The downstream effects of NUTM1r include upregulation of the proto-oncogene BMI1 and specific fusions also induce transcription of the HOXA gene cluster (Hormann et al. Haematologica 2019; Li et al. PNAS 2018). This novel subtype is rare in children, but appears to be more prevalent among infants negative for KMT2A rearrangement (KMT2Ar) based on the frequency of karyotypic 15q aberrations (De Lorenzo et al. Leukemia 2014). This international collaborative study aimed to determine the frequency of NUTM1r in infant and pediatric cohorts, and to characterize the demographic, clinical and molecular features of NUTM1r-positive B-ALL. Patients and Methods Interfant-related study groups provided NUTM1 screening results for KMT2Ar-negative Interfant-99 and -06 cases with karyotypic 15q aberration, normal karyotype, or missing karyotype. Additionally, NUTM1r-positive cases of any age were collected from the study groups united in the Ponte di Legno consortium. The identified NUTM1r-positive children were diagnosed between 1995-2019, infants (≤365 days of age) included in the Interfant-99 or 06 trials were diagnosed between 2000-2016, and remaining infants between 1986-2019. The techniques used for the detection of NUTM1r were break-apart FISH, RNA sequencing, and RT-PCR. Event-free survival (EFS) and overall survival (OS) were estimated according to Kaplan-Meier, standard error according to Greenwood, and the curves were compared by log-rank test. Results We identified 81 NUTM1r cases, including 35 Interfant-enrolled infants, 10 other infants and 36 children. NUTM1r was reported to be rare among pediatric B-ALL with an estimated frequency range of 0.28-0.86%. The median age among NUTM1r-positive children was 4.5 years (range 1-15). Among KMT2Ar-negative infants the frequency of NUTM1r was 21.7%. Of NUTM1r-positive infants, 54% were Of the NUTM1r-positive cases, all achieved complete remission, 82% had minimal residual disease In order of frequency, NUTM1 fusion partners were ACIN1 (30.4%), CUX1 (21.7%), BRD9 (17.4%), ZNF618 (13%), AFF1 (4.3%), SLC12A6 (4.3%), IKZF1 (2.9%), and three novel partners: ATAD5 (2.9%), CHD4 (1.4%) and RUNX1 (1.4%). Infants mainly showed fusions with ACIN1, CUX1, BRD9 and AFF1, associated with HOXA9 upregulation. Older infants and children showed both HOXA-upregulating and non-HOXA-upregulating fusions. Epigenetic profiling showed a distinct pattern of DNA methylation and histone modification of the HOXA gene cluster region in leukemic cells of an ACIN1-NUTM1 pediatric case compared with KMT2Ar-positive and KMT2Ar/NUTM1r-negative pediatric cases. Conclusions NUTM1r ALL was identified as the second largest subtype in infants, found in 21.7% of KMT2Ar-negative infant B-ALL, representing 5-7% of total infant ALL, and associated with excellent outcome on Interfant standard risk protocols. The favorable outcome was confirmed in the Ponte di Legno cohort of infant and pediatric NUTM1r-positive patients enrolled on different treatment protocols over more than two decades. We conclude that NUTM1r ALL is a favorable genetic subtype in infants and children and possibly eligible for treatment reduction. Disclosures No relevant conflicts of interest to declare.